Merge branch 'feature/compatibility' of https://github.com/tommydeboe…

…r/molgenis-tools-commander into feature/language

mcmd/client/api.py

@@ -0,0 +1,85 @@
+from urllib.parse import urljoin
+
+from mcmd.config import config
+from mcmd.version.compatibility import version
+
+
+def endpoint(func):
+    def wrapper():
+        return urljoin(config.get('host', 'selected'), func())
+
+    return wrapper
+
+
+@endpoint
+def rest1():
+    return 'api/v1/'
+
+
+@endpoint
+def rest2():
+    return 'api/v2/'
+
+
+@endpoint
+def login():
+    return 'api/v1/login/'
+
+
+@endpoint
+@version('7.0.0')
+def group():
+    return 'api/plugin/security/group/'
+
+
+@endpoint
+@version('8.0.0')
+def group():
+    return 'api/identities/v1/group/'
+
+
+@endpoint
+@version('7.0.0')
+def member(group_name):
+    return 'api/plugin/security/group/{}/member/'.format(group_name)
+
+
+@endpoint
+@version('8.0.0')
+def member(group_name):
+    return 'api/identities/v1/group/{}/member/'.format(group_name)
+
+
+@endpoint
+def import_():
+    return 'plugin/importwizard/importFile/'
+
+
+@endpoint
+def import_by_url():
+    return 'plugin/importwizard/importByUrl/'
+
+
+@endpoint
+def permissions():
+    return 'menu/admin/permissionmanager/update/'
+
+
+@endpoint
+def rls():
+    return 'menu/admin/permissionmanager/update/entityclass/rls'
+
+
+@endpoint
+def add_theme():
+    return 'plugin/thememanager/add-bootstrap-theme'
+
+
+@endpoint
+def set_theme():
+    return 'plugin/thememanager/set-bootstrap-theme'
+
+
+@endpoint
+def logo():
+    return 'plugin/menumanager/upload-logo'

mcmd/client/auth.py

@@ -10,8 +10,9 @@
 from requests import HTTPError
 
 from mcmd import io
+from mcmd.client import api
 from mcmd.config import config
-from mcmd.utils.errors import McmdError
+from mcmd.utils.errors import McmdError, MolgenisOfflineError
 
 _username = None
 _password = None
@@ -40,7 +41,7 @@ def check_token():
         return
 
     try:
-        response = requests.get(urljoin(config.api('rest2'), 'sys_sec_Token?q=token=={}'.format(_token)),
+        response = requests.get(urljoin(api.rest2(), 'sys_sec_Token?q=token=={}'.format(_token)),
                                 headers={'Content-Type': 'application/json', 'x-molgenis-token': _token})
         response.raise_for_status()
     except HTTPError as e:
@@ -49,7 +50,7 @@ def check_token():
         else:
             raise McmdError(str(e))
     except requests.exceptions.ConnectionError:
-        raise McmdError("Can't connect to {}".format(config.url()))
+        raise MolgenisOfflineError()
 
 
 def _login():
@@ -61,7 +62,7 @@ def _login():
 
     try:
         io.debug('Logging in as user {}'.format(_username))
-        response = requests.post(config.api('login'),
+        response = requests.post(api.login(),
                                  headers={'Content-Type': 'application/json'},
                                  data=json.dumps({"username": _username, "password": _password}))
         response.raise_for_status()

mcmd/client/molgenis_client.py

@@ -1,42 +1,44 @@
 import json
-from urllib.parse import urljoin
 
 import requests
 
 from mcmd.client import auth
 from mcmd.client.request_handler import request
-from mcmd.config import config
 
 
-@request()
+@request
 def get(url):
     return requests.get(url,
                         headers=_get_default_headers())
 
 
-@request()
-def post(url, data):
-    return requests.post(url,
-                         headers=_get_default_headers(),
-                         data=json.dumps(data))
+@request
+def post(url, data=None, params=None):
+    kwargs = {'headers': _get_default_headers()}
+    if data:
+        kwargs['data'] = json.dumps(data)
+    if params:
+        kwargs['params'] = params
+
+    return requests.post(url, **kwargs)
 
 
-@request()
+@request
 def post_file(url, file_path, params):
     return requests.post(url,
                          headers={'x-molgenis-token': auth.get_token()},
                          files={'file': open(file_path, 'rb')},
                          params=params)
 
 
-@request()
+@request
 def post_files(files, url):
     return requests.post(url,
                          headers={'x-molgenis-token': auth.get_token()},
                          files=files)
 
 
-@request()
+@request
 def post_form(url, data):
     return requests.post(url,
                          headers={
@@ -45,39 +47,26 @@ def post_form(url, data):
                          data=data)
 
 
-@request()
+@request
 def delete(url):
     return requests.delete(url,
                            headers=_get_default_headers())
 
 
-@request()
+@request
 def delete_data(url, data):
     return requests.delete(url,
                            headers=_get_default_headers(),
                            data=json.dumps({"entityIds": data}))
 
 
-@request()
+@request
 def put(url, data):
     return requests.put(url=url,
                         headers=_get_default_headers(),
                         data=data)
 
 
-@request()
-def import_by_url(params):
-    return requests.post(config.api('import_url'),
-                         headers=_get_default_headers(),
-                         params=params)
-
-
-@request(login=False)
-def get_version():
-    return requests.get(urljoin(config.api('rest2'), 'version'),
-                        headers={'Content-Type': 'application/json'})
-
-
 def _get_default_headers():
     headers = {'Content-Type': 'application/json',
                'x-molgenis-token': auth.get_token()}

mcmd/client/request_handler.py

@@ -7,37 +7,31 @@
 import requests
 
 from mcmd.client import auth
-from mcmd.config import config
-from mcmd.utils.errors import McmdError
+from mcmd.utils.errors import McmdError, MolgenisOfflineError
 
 
-def request(login=True):
+def request(func):
     """Request decorator."""
 
-    def decorator(func):
-
-        def handle_request(*args, **kwargs):
-            if login:
-                auth.check_token()
-
-            response = str()
-            try:
-                response = func(*args, **kwargs)
-                response.raise_for_status()
-                return response
-            except requests.HTTPError as e:
-                if _is_json(response):
-                    _handle_json_error(response.json())
-                else:
-                    raise McmdError(str(e))
-            except requests.exceptions.ConnectionError:
-                raise McmdError("Can't connect to {}".format(config.url()))
-            except requests.RequestException as e:
+    def handle_request(*args, **kwargs):
+        auth.check_token()
+
+        response = str()
+        try:
+            response = func(*args, **kwargs)
+            response.raise_for_status()
+            return response
+        except requests.HTTPError as e:
+            if _is_json(response):
+                _handle_json_error(response.json())
+            else:
                 raise McmdError(str(e))
+        except requests.exceptions.ConnectionError:
+            raise MolgenisOfflineError()
+        except requests.RequestException as e:
+            raise McmdError(str(e))
 
-        return handle_request
-
-    return decorator
+    return handle_request
 
 
 def _handle_json_error(response_json):

mcmd/commands/add.py

@@ -4,6 +4,7 @@
 
 import mcmd.config.config as config
 from mcmd import io
+from mcmd.client import api
 from mcmd.client.molgenis_client import post, get, post_files
 from mcmd.command import command
 from mcmd.commands._registry import arguments
@@ -131,20 +132,20 @@ def add_user(args):
     superuser = args.is_superuser
     ch_pwd = args.change_password
 
-    post(config.api('rest1') + 'sys_sec_User',
-         {'username': args.username,
-          'password_': password,
-          'changePassword': ch_pwd,
-          'Email': email,
-          'active': active,
-          'superuser': superuser
-          })
+    post(api.rest1() + 'sys_sec_User',
+         data={'username': args.username,
+               'password_': password,
+               'changePassword': ch_pwd,
+               'Email': email,
+               'active': active,
+               'superuser': superuser
+               })
 
 
 @command
 def add_group(args):
     io.start('Adding group %s' % highlight(args.name))
-    post(config.api('group'), {'name': args.name.lower(), 'label': args.name})
+    post(api.group(), data={'name': args.name.lower(), 'label': args.name})
 
 
 @command
@@ -157,14 +158,14 @@ def add_package(args):
     if args.parent:
         data['parent'] = args.parent
 
-    post(config.api('rest1') + 'sys_md_Package', data)
+    post(api.rest1() + 'sys_md_Package', data=data)
 
 
 @command
 def add_token(args):
     io.start('Adding token %s for user %s' % (highlight(args.token), highlight(args.user)))
 
-    user = get(config.api('rest2') + 'sys_sec_User?attrs=id&q=username==%s' % args.user)
+    user = get(api.rest2() + 'sys_sec_User?attrs=id&q=username==%s' % args.user)
     if user.json()['total'] == 0:
         raise McmdError('Unknown user %s' % args.user)
 
@@ -173,7 +174,7 @@ def add_token(args):
     data = {'User': user_id,
             'token': args.token}
 
-    post(config.api('rest1') + 'sys_sec_Token', data)
+    post(api.rest1() + 'sys_sec_Token', data=data)
 
 
 @command
@@ -185,7 +186,7 @@ def add_theme(args):
     """
     _validate_args(args)
     valid_types = {'text/css'}
-    api = config.api('add_theme')
+    api_ = api.add_theme()
     bs3_name = args.bootstrap3
     bs4 = args.bootstrap4
     paths = [bs3_name]
@@ -205,7 +206,7 @@ def add_theme(args):
     if not args.from_path:
         paths = [_get_path_from_quick_folders(theme) for theme in paths]
     files = _prepare_files_for_upload(paths, names, valid_types)
-    post_files(files, api)
+    post_files(files, api_)
 
 
 @command
@@ -215,7 +216,7 @@ def add_logo(args):
     :param args: commandline arguments containing path to logo
     :return: None
     """
-    api = config.api('logo')
+    api_ = api.logo()
     valid_types = {'image/jpeg', 'image/png', 'image/gif'}
     logo = [args.logo]
     if not args.from_path:
@@ -224,7 +225,7 @@ def add_logo(args):
     else:
         io.start('Adding logo {}'.format(highlight(args.logo)))
     files = _prepare_files_for_upload(logo, ['logo'], valid_types)
-    post_files(files, api)
+    post_files(files, api_)
 
 
 def _prepare_files_for_upload(paths, names, valid_content_types):